Iridium in PDB 5de8: Crystal Structure of the Complex Between Human Fmrp Rgg Motif and G- Quadruplex Rna, Iridium Hexammine Bound Form.

The structure of Crystal Structure of the Complex Between Human Fmrp Rgg Motif and G- Quadruplex Rna, Iridium Hexammine Bound Form., PDB code: 5de8 was solved by N.Vasilyev, A.Polonskaia, J.C.Darnell, R.B.Darnell, D.J.Patel, A.Serganov, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.36 / 3.10
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	57.650, 130.600, 36.700, 90.00, 90.00, 90.00
R / Rfree (%)	20.1 / 22.7

The structure of Crystal Structure of the Complex Between Human Fmrp Rgg Motif and G- Quadruplex Rna, Iridium Hexammine Bound Form. also contains other interesting chemical elements:

Potassium

(K)

2 atoms

The binding sites of Iridium atom in the Crystal Structure of the Complex Between Human Fmrp Rgg Motif and G- Quadruplex Rna, Iridium Hexammine Bound Form. (pdb code 5de8). This binding sites where shown within 5.0 Angstroms radius around Iridium atom.
In total 5 binding sites of Iridium where determined in the Crystal Structure of the Complex Between Human Fmrp Rgg Motif and G- Quadruplex Rna, Iridium Hexammine Bound Form., PDB code: 5de8:
Jump to Iridium binding site number: 1; 2; 3; 4; 5;

Iridium binding site 1 out of 5 in the Crystal Structure of the Complex Between Human Fmrp Rgg Motif and G- Quadruplex Rna, Iridium Hexammine Bound Form.


Mono view


Stereo pair view

A full contact list of Iridium with other atoms in the Ir binding site number 1 of Crystal Structure of the Complex Between Human Fmrp Rgg Motif and G- Quadruplex Rna, Iridium Hexammine Bound Form. within 5.0Å range: probe atom residue distance (Å) B Occ A:Ir102 b:0.1 occ:0.68 IR A:IRI102 0.0 0.1 0.7 N4 A:IRI102 2.0 0.5 0.7 N3 A:IRI102 2.0 0.4 0.7 N5 A:IRI102 2.0 0.9 0.7 N6 A:IRI102 2.0 0.4 0.7 N2 A:IRI102 2.0 0.6 0.7 N1 A:IRI102 2.0 65.6 0.7 OP2 A:A13 3.8 47.3 1.0 OP1 A:A13 4.3 43.2 1.0 P A:A13 4.6 50.8 1.0 OP1 A:U8 4.8 63.6 1.0 C2 A:A13 5.0 73.4 1.0

Iridium binding site 2 out of 5 in the Crystal Structure of the Complex Between Human Fmrp Rgg Motif and G- Quadruplex Rna, Iridium Hexammine Bound Form.


Mono view


Stereo pair view

A full contact list of Iridium with other atoms in the Ir binding site number 2 of Crystal Structure of the Complex Between Human Fmrp Rgg Motif and G- Quadruplex Rna, Iridium Hexammine Bound Form. within 5.0Å range: probe atom residue distance (Å) B Occ A:Ir103 b:0.3 occ:0.43 IR A:IRI103 0.0 0.3 0.4 N6 A:IRI103 2.0 82.4 0.4 N1 A:IRI103 2.0 4.5 0.4 N2 A:IRI103 2.0 55.4 0.4 N4 A:IRI103 2.0 73.8 0.4 N3 A:IRI103 2.0 49.1 0.4 N5 A:IRI103 2.0 0.2 0.4 OP2 A:U27 3.4 55.9 1.0 OP2 A:C22 3.5 33.6 1.0 N1 A:IRI104 3.5 0.3 0.6 OP2 A:U28 3.6 41.5 1.0 N2 A:IRI104 3.9 77.4 0.6 O2 A:U27 4.0 97.5 1.0 O4' A:U27 4.0 74.1 1.0 OP1 A:G24 4.3 32.3 1.0 O2' A:G26 4.6 46.1 1.0 P A:U27 4.6 40.0 1.0 C2 A:U27 4.7 0.3 1.0 IR A:IRI104 4.8 0.5 0.6 O3' A:G26 4.8 41.2 1.0 C1' A:U27 4.8 89.3 1.0 P A:C22 4.8 33.5 1.0 C4' A:U27 4.9 81.2 1.0 N5 A:IRI104 4.9 67.2 0.6 O3' A:G21 5.0 37.9 1.0

Iridium binding site 3 out of 5 in the Crystal Structure of the Complex Between Human Fmrp Rgg Motif and G- Quadruplex Rna, Iridium Hexammine Bound Form.


Mono view


Stereo pair view

A full contact list of Iridium with other atoms in the Ir binding site number 3 of Crystal Structure of the Complex Between Human Fmrp Rgg Motif and G- Quadruplex Rna, Iridium Hexammine Bound Form. within 5.0Å range: probe atom residue distance (Å) B Occ A:Ir104 b:0.5 occ:0.59 IR A:IRI104 0.0 0.5 0.6 N1 A:IRI104 2.0 0.3 0.6 N6 A:IRI104 2.0 82.0 0.6 N2 A:IRI104 2.0 77.4 0.6 N4 A:IRI104 2.0 64.5 0.6 N5 A:IRI104 2.0 67.2 0.6 N3 A:IRI104 2.0 0.4 0.6 N6 A:IRI103 3.6 82.4 0.4 N1 A:IRI103 3.8 4.5 0.4 OP1 A:G24 4.1 32.3 1.0 OP2 A:U27 4.2 55.9 1.0 OP1 A:G25 4.8 58.2 1.0 IR A:IRI103 4.8 0.3 0.4 N4 A:IRI103 4.8 73.8 0.4 OP2 A:G25 5.0 31.7 1.0

Iridium binding site 4 out of 5 in the Crystal Structure of the Complex Between Human Fmrp Rgg Motif and G- Quadruplex Rna, Iridium Hexammine Bound Form.


Mono view


Stereo pair view

A full contact list of Iridium with other atoms in the Ir binding site number 4 of Crystal Structure of the Complex Between Human Fmrp Rgg Motif and G- Quadruplex Rna, Iridium Hexammine Bound Form. within 5.0Å range: probe atom residue distance (Å) B Occ C:Ir102 b:0.0 occ:0.53 IR C:IRI102 0.0 0.0 0.5 N5 C:IRI102 2.0 35.6 0.5 N4 C:IRI102 2.0 34.3 0.5 N6 C:IRI102 2.0 42.4 0.5 N3 C:IRI102 2.0 70.4 0.5 N2 C:IRI102 2.0 48.7 0.5 N1 C:IRI102 2.0 27.6 0.5 OP1 C:U8 3.5 61.0 1.0 OP2 C:A13 4.3 50.3 1.0 OP1 C:G9 4.4 41.0 1.0 OP2 C:G9 4.6 40.4 1.0 OP1 C:A13 4.7 75.3 1.0 P C:U8 4.8 60.1 1.0 P C:G9 4.9 58.2 1.0 P C:A13 5.0 42.4 1.0

Iridium binding site 5 out of 5 in the Crystal Structure of the Complex Between Human Fmrp Rgg Motif and G- Quadruplex Rna, Iridium Hexammine Bound Form.


Mono view


Stereo pair view

A full contact list of Iridium with other atoms in the Ir binding site number 5 of Crystal Structure of the Complex Between Human Fmrp Rgg Motif and G- Quadruplex Rna, Iridium Hexammine Bound Form. within 5.0Å range: probe atom residue distance (Å) B Occ C:Ir103 b:0.9 occ:0.55 IR C:IRI103 0.0 0.9 0.6 N1 C:IRI103 2.0 0.3 0.6 N5 C:IRI103 2.0 80.2 0.6 N2 C:IRI103 2.0 47.9 0.6 N4 C:IRI103 2.0 0.6 0.6 N3 C:IRI103 2.0 0.1 0.6 N6 C:IRI103 2.0 87.7 0.6 O2' C:G6 3.7 40.6 1.0 OP2 C:G7 3.8 56.8 1.0 O3' C:G6 4.0 52.5 1.0 OP1 C:G15 4.5 37.6 1.0 OP2 C:G16 4.5 34.6 1.0 P C:G7 4.6 42.0 1.0 C2' C:G6 4.8 33.9 1.0 O3' C:G15 4.9 34.4 1.0 C3' C:G6 4.9 36.2 1.0

N.Vasilyev, A.Polonskaia, J.C.Darnell, R.B.Darnell, D.J.Patel, A.Serganov. Crystal Structure Reveals Specific Recognition of A G-Quadruplex Rna By A Beta-Turn in the Rgg Motif of Fmrp. Proc.Natl.Acad.Sci.Usa V. 112 E5391 2015.
ISSN: ESSN 1091-6490
PubMed: 26374839
DOI: 10.1073/PNAS.1515737112